Chromosome-Scale Assembly of the Complete Genome Sequence of
 Leishmania
 (
 Mundinia
 )
 martiniquensis
 , Isolate LSCM1, Strain LV760

Almutairi, Hatim; Urbaniak, Michael D.; Bates, Michelle; Jariyapan, Narissara; Al-Salem, Waleed S.; Dillon, Rod J.; Bates, Paul A.; Gatherer, Derek

doi:10.1128/mra.00058-21

Cited by 7 publications

(8 citation statements)

References 22 publications

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“…This study also found that the de Bruijn graph-based MEGAHIT program was another good assembler for the Leishmania genome compared to SPAdes which was used several times in our workflow, consistent with the report that the MEGAHIT program could handle large and complex next-generation sequencing datasets [ 51 ]. In contrast, several recent chromosome-scale Leishmania genomes, including L. orientalis isolate LSCM4, were assembled using de novo assembly of the long-read MinION data as guidance for mapping the Illumina short reads [ 45 ]. In this study, our assembled genome of L. orientalis isolates PCM2 from the proposed analytic workflow on the short-read data shared highly similar genomic synteny with those of the LSCM4, as shown in Figure 3 , implying the genome structural similarity between the selected reference, L. enriettii , and the LSCM4 genome.…”

Section: Discussionmentioning

confidence: 99%

“…Despite concerns about the genetic variation of L. orientalis and their public health impacts, genomic information of multiple L. orientalis isolates has gained attention. To date, three major genome sequencing platforms (Illumina, PacBio, and Oxford Nanopore) have been used to create the complete genomic data of several Leishmania species, including the genome of L. major strain Friedlin [ 31 , 42 , 43 , 44 ], L. infantum strain JPCM5 [ 33 , 42 ], L. martiniquensis strain LSCM1 [ 45 , 46 , 47 ], and a recent L. orientalis strain LSCM4 isolated from the northern province of Thailand [ 46 , 47 , 48 ], in exchange for considerable cost invested in the genome project. Questions have arisen on whether the new Leishmania species shall have their whole genomes decoded using all techniques at first glance.…”

Section: Introductionmentioning

confidence: 99%

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Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand

Anuntasomboon

Siripattanapipong

Unajak

et al. 2022

Biology

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Background: Leishmania orientalis (formerly named Leishmania siamensis) has been neglected for years in Thailand. The genomic study of L. orientalis has gained much attention recently after the release of the first high-quality reference genome of the isolate LSCM4. The integrative approach of multiple sequencing platforms for whole-genome sequencing has proven effective at the expense of considerably expensive costs. This study presents a preliminary bioinformatic workflow including the use of multi-step de novo assembly coupled with the reference-based assembly method to produce high-quality genomic drafts from the short-read Illumina sequence data of L. orientalis isolate PCM2. Results: The integrating multi-step de novo assembly by MEGAHIT and SPAdes with the reference-based method using the L. enriettii genome and salvaging the unmapped reads resulted in the 30.27 Mb genomic draft of L. orientalis isolate PCM2 with 3367 contigs and 8887 predicted genes. The results from the integrated approach showed the best integrity, coverage, and contig alignment when compared to the genome of L. orientalis isolate LSCM4 collected from the northern province of Thailand. Similar patterns of gene ratios and frequency were observed from the GO biological process annotation. Fifty GO terms were assigned to the assembled genomes, and 23 of these (accounting for 61.6% of the annotated genes) showed higher gene counts and ratios when results from our workflow were compared to those of the LSCM4 isolate. Conclusions: These results indicated that our proposed bioinformatic workflow produced an acceptable-quality genome of L. orientalis strain PCM2 for functional genomic analysis, maximising the usage of the short-read data. This workflow would give extensive information required for identifying strain-specific markers and virulence-associated genes useful for drug and vaccine development before a more exhaustive and expensive investigation.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand

Anuntasomboon

Siripattanapipong

Unajak

et al. 2022

Biology

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“…Recently, highly accurate genomes for L. martiniquensis and L . orientalis, isolated in northern Thailand, were reported [ 54 , 55 ]. In this study, however, candidate antigens were selected based on the data from draft genomes of the two species isolated in southern Thailand [ 25 ], and more candidates may be found if highly accurate sequence information becomes available.…”

Section: Discussionmentioning

confidence: 99%

Design of a Chimeric Multi-Epitope Vaccine (CMEV) against Both Leishmania martiniquensis and Leishmania orientalis Parasites Using Immunoinformatic Approaches

Imaizumi

Phurahong

Siripattanapipong

et al. 2022

Biology

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Leishmaniasis is a parasitic disease caused by protozoan flagellates of the genus Leishmania. Recently, Leishmania martiniquensis and Leishmania orientalis, emerging species of Leishmania, were isolated from patients in Thailand. Development of the vaccine is demanded; however, genetic differences between the two species make it difficult to design a vaccine that is effective for both species. In this study, we applied immuno-informatic approaches to design a chimeric multi-epitope vaccine (CMEV) against both L. martiniquensis and L. orientalis. We identified seven helper T lymphocyte (HTL) epitopes, sixteen cytotoxic T lymphocyte (CTL) epitopes, and eleven B-cell epitopes from sixteen conserved antigenic proteins found in both species. All these epitopes were joined together, and to further enhance immunogenicity, protein and peptides adjuvant were also added at the N-terminal of the molecule by using specific linkers. The candidate CMEV was subsequently analyzed from the perspectives of the antigenicity, allergenicity, and physiochemical properties. The interaction of the designed multi-epitope vaccine and immune receptor (TLR4) of the host were evaluated based on molecular dockings of the predicted 3D structures. Finally, in silico cloning was performed to construct the expression vaccine vector. Docking analysis showed that the vaccine/TLR4 complex took a stable form. Based on the predicted immunogenicity, physicochemical, and structural properties in silico, the vaccine candidate was expected to be appropriately expressed in bacterial expression systems and show the potential to induce a host immune response. This study proposes the experimental validation of the efficacy of the candidate vaccine construct against the two Leishmania.

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“…De novo assembly was performed using SPAdes version 3.12.0 [ 20 ]. The scaffold sequences from the previous step were used to align with the Leishmania martiniquensis genome from the NCBI database (accession number CM030396.1–CM030431.1 for chromosome 1–36) [ 21 ] using the Artemis comparison tool (ACT) [ 22 ]. In addition, the Illumina reads were mapped into the assembled scaffolds using BWA version 0.7.16a [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

Genome Assembly and Genome Annotation of Leishmania martiniquensis Isolated from a Leishmaniasis Patient in Thailand

Anuntakarun

Phumee

Sawaswong

et al. 2022

Journal of Parasitology Research

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Leishmaniasis is a parasitic disease caused by Leishmania spp. with worldwide distribution. Autochthonous leishmaniasis has been reported to result from the infection by Leishmania martiniquensis in Thailand. This species was isolated in culture and subjected to high-throughput whole-genome sequencing. A total of 30.8 Mb in 36 chromosomes of the whole genome was assembled, annotated, and characterized. The L. martiniquensis under study was shown to segregate into the same clade and thus closely related to the previously identified L. martiniquensis (LU_Lmar_1.0), as determined by phylogenetic analysis of their genomic sequences along with those of representative kinetoplastid species. The total number of open reading frames genomewide predicts 8,209 protein-coding genes, of which 359 are putative virulence factors, including two previously known, e.g., cysteine proteinase C and superoxide dismutase B1. The results obtained from this study will be useful for further annotation and comparison with other Leishmania martiniquensis in the future.

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Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania ( Mundinia ) martiniquensis , Isolate LSCM1, Strain LV760

Cited by 7 publications

References 22 publications

Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand

Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand

Design of a Chimeric Multi-Epitope Vaccine (CMEV) against Both Leishmania martiniquensis and Leishmania orientalis Parasites Using Immunoinformatic Approaches

Genome Assembly and Genome Annotation of Leishmania martiniquensis Isolated from a Leishmaniasis Patient in Thailand

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